OAK RIDGE, Tenn., Dec. 9, 2010 -- A quicker and cheaper technique to scan molecular databases developed at the Department of Energy's Oak Ridge National Laboratory could put scientists on the fast track to developing new drug treatments.
A team led by Jerome Baudry of the University of Tennessee-ORNL Center for Molecular Biophysics adapted a widely used existing software to allow supercomputers such as ORNL's Jaguar to sift through immense molecular databases and pinpoint chemical compounds as potential drug candidates.
The research was published in the Journal of Computational Chemistry as "Task-parallel MPI implementation of Autodock4 for docking of very large databases of compounds using High Performance Super-Computers."
"Our research is the missing link between supercomputers and the huge data available in molecular databases like the Human Genome Project," Baudry said. "We have an avalanche of data available to us, and now we need to translate that data into knowledge."
Such translation is critical for the first stages of drug development, in which researchers look for appropriate chemicals that interact with a target in the body, typically a protein. If the chemical is suitable, it attaches onto the protein and produces a desirable effect in the cell.
But with thousands of known proteins and millions of chemicals as potential drugs, the number of possible combinations is astronomical.
"It is very expensive and time-consuming to measure these interactions experimentally," Baudry said. "But with supercomputers, we can process millions of molecules a day."
The quick and efficient processing of molecules offers scientists an opportunity to take risks on previously unexamined drug candidates, which could lead to diverse and innovative classes of drugs.
"Before, we threw away a lot of information because molecules did not have a preferred profile," Baudry said. "Now, every
|Contact: Morgan McCorkle|
DOE/Oak Ridge National Laboratory